[Hackathon] Re: [Bioperl-l] proposed change to Bio::SeqFeature::Gene::*

Chris Mungall cjm at fruitfly.org
Wed Jun 18 15:17:45 EDT 2003

On 18 Jun 2003, Mark Wilkinson wrote:

> On Wed, 2003-06-18 at 14:57, Lincoln Stein wrote:
> > The idea for GFF3 is that the third column becomes controlled by an ontology
> > AND is used as the primary_tag.  I guess this implies that the primary_tag
> > becomes controlled by an ontology.
> Only for features that are created from GFF3... which is the problem.
> At the moment primary_tag is not *reliable* in representing what type of
> feature object it is attached to.

sure, there would probably be a type mapping stage involved. There is
already a gb feature type -> SO mapping.

This mapping would have to take place one way or another, whether it is
unreliable type -> perl class; or unreliably type -> SO term

> >   The aggregator/fluffer/unflattener should
> I'm not sure that "fluffer" is such a good idea given the vernacular
> meaning of the word...  :-)
> (...or perhaps I should be ashamed of possessing this kind of
> knowledge??)

Hey, we know how it is. You've got to pay your way though college somehow.

> Mark


More information about the Bioperl-l mailing list